Read Thread: Unread messages dissapearing
Are you using threads? Because those thread links don't work well with favorite boards.
The other problem might be if you're using that new link to "view recent messages." If you view recent messages, it won't show you all of your unread messages--just the most recently posted ones--but it'll cause all messages before that to become old.
Actually, that also happens if you read individual messages directly from My Page. Any message posted before the one you open is marked as "old."
I think I'm going to stop messing with the message boards and not put up anymore changes until they're completely done and revamped. I can see I'm confusing too many people with these incremental changes!